sRNA Seq Step 1: Read Pre Processing And Removal Of Artifacts (no Grooming) Version 1
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Steps
| ID | Name | Description |
|---|---|---|
| 3 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65 |
| 4 | Trim Galore! | toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.2 |
| 5 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65 |
| 6 | HISAT | Alignment of reads against rRNA sequences to filter them out. toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3 |
| 7 | Filter SAM or BAM, output SAM or BAM | Keep reads that did NOT align to rRNA sequences. toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.2 |
| 8 | Convert from BAM to FastQ | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0 |
| 9 | HISAT | toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3 |
| 10 | Filter SAM or BAM, output SAM or BAM | Keep reads that did NOT align to miRNA sequences. toolshed.g2.bx.psu.edu/repos/devteam/samtool_filter2/samtool_filter2/1.1.2 |
| 11 | Convert from BAM to FastQ | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_bamtofastq/2.24.0 |
| 12 | Manipulate FASTQ | toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.0.1 |
| 13 | Manipulate FASTQ | toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.0.1 |
| 14 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65 |
| 15 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.65 |
Version History
2 (earliest) Created 22nd Apr 2024 at 11:10 by Helena Rasche
Added/updated 3 files
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Created: 22nd Apr 2024 at 11:10
Last updated: 22nd Apr 2024 at 11:10
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